Protein-protein interactions: detection, reliability assessment and applications

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Briefings Bioinform.

• Publication date

  2016-07-21

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bib/bbw066PMID 27444371
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Predicting Protein-Protein Interactions from the Molecular to the Proteome Level.

  2016cited by this paper
• Probing the Small-Molecule Inhibition of an Anticancer Therapeutic Protein-Protein Interaction Using a Solid-State Nanopore.

  2016cited by this paper
• A High-Throughput Screening Strategy to Identify Protein-Protein Interaction Inhibitors That Block the Fanconi Anemia DNA Repair Pathway

  2016cited by this paper
• Exploring novel mechanistic insights in Alzheimer’s disease by assessing reliability of protein interactions

  2015cited by this paper
• Discovery of New Candidate Genes Related to Brain Development Using Protein Interaction Information

  2015cited by this paper
• Evolutionary profiles improve protein-protein interaction prediction from sequence

  2015cited by this paper
• Next-Generation Sequencing for Binary Protein–Protein Interactions

  2015cited by this paper
• Large-scale identification of potential drug targets based on the topological features of human protein-protein interaction network.

  2015cited by this paper
• Discovery of pathways in protein-protein interaction networks using a genetic algorithm

  2015cited by this paper
• Developing Antagonists for the Met-HGF/SF Protein–Protein Interaction Using a Fragment-Based Approach

  2015cited by this paper
• Tumor Grafting Induces Changes of Gut Microbiota in Athymic Nude Mice in the Presence and Absence of Medicinal Gynostemma Saponins

  2015cited by this paper
• The Roles of Post-translational Modifications in the Context of Protein Interaction Networks

  2015cited by this paper
• Precision medicine for cancer with next-generation functional diagnostics

  2015cited by this paper
• An efficient method to identify essential proteins for different species by integrating protein subcellular localization information

  2015cited by this paper
• Illuminating Spatial and Temporal Organization of Protein Interaction Networks by Mass Spectrometry-Based Proteomics

  2015cited by this paper
• Prediction and redesign of protein-protein interactions.

  2014cited by this paper
• Predicting Essential Proteins Based on Weighted Degree Centrality

  2014cited by this paper
• Protein interaction switches coordinate Raf-1 and MST2/Hippo signalling

  2014cited by this paper
• Small-Molecule Inhibitors of the MDM2–p53 Protein–Protein Interaction (MDM2 Inhibitors) in Clinical Trials for Cancer Treatment

  2014cited by this paper
• Dynamic protein interaction network construction and applications

  2014cited by this paper
• Bioinformatics Research and Applications

  2014cited by this paper
• Prediction of Protein–Protein Interaction with Pairwise Kernel Support Vector Machine

  2014cited by this paper
• Targeting protein-protein interaction by small molecules.

  2014cited by this paper
• Exploring Function Prediction in Protein Interaction Networks via Clustering Methods

  2014cited by this paper
• A Large Scale Huntingtin Protein Interaction Network Implicates Rho GTPase Signaling Pathways in Huntington Disease*♦

  2014cited by this paper
• In silico prediction of physical protein interactions and characterization of interactome orphans

  2014cited by this paper
• Using Topology Information for Protein-Protein Interaction Prediction

  2014cited by this paper
• The BioGRID interaction database: 2015 update

  2014cited by this paper
• Protein-Protein Interaction Detection: Methods and Analysis

  2014cited by this paper
• Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine

  2014cited by this paper
• A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity

  2013cited by this paper
• A Y2H-seq approach defines the human protein methyltransferase interactome

  2013cited by this paper
• Self-Healing Efficiency of Cementitious Materials Containing Microcapsules Filled with Healing Adhesive: Mechanical Restoration and Healing Process Monitored by Water Absorption

  2013cited by this paper
• Examining post‐translational modification‐mediated protein–protein interactions using a chemical proteomics approach

  2013cited by this paper
• Computational Prediction of Protein–Protein Interaction Networks: Algo-rithms and Resources

  2013cited by this paper
• Complementing the Eukaryotic Protein Interactome

  2013cited by this paper
• Genotype-phenotype relationships in light of a modular protein interaction landscape.

  2013cited by this paper
• ppiPre: predicting protein-protein interactions by combining heterogeneous features

  2013cited by this paper
• Signal Propagation in Protein Interaction Network during Colorectal Cancer Progression

  2013cited by this paper
• Construction and application of dynamic protein interaction network based on time course gene expression data

  2013cited by this paper
• Protein complex detection using interaction reliability assessment and weighted clustering coefficient

  2013cited by this paper
• Protein Interaction Network of the Mammalian Hippo Pathway Reveals Mechanisms of Kinase-Phosphatase Interactions

  2013cited by this paper
• Promise of personalized omics to precision medicine

  2013cited by this paper
• Investigation of stable and transient protein–protein interactions: Past, present, and future

  2013cited by this paper
• Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions

  2013cited by this paper
• Prioritizing Disease Candidate Proteins in Cardiomyopathy-Specific Protein-Protein Interaction Networks Based on “Guilt by Association” Analysis

  2013cited by this paper
• Structural biology. Versatility from protein disorder.

  2012cited by this paper
• Intrinsic Protein Disorder and Protein-Protein Interactions

  2012cited by this paper
• Versatility from Protein Disorder

  2012cited by this paper
• IntScore: a web tool for confidence scoring of biological interactions

  2012cited by this paper
• Structure-based prediction of protein-protein interactions on a genome-wide scale

  2012cited by this paper
• Mass spectrometry-based proteomics and network biology.

  2012cited by this paper
• Diversity in Genetic In Vivo Methods for Protein-Protein Interaction Studies: from the Yeast Two-Hybrid System to the Mammalian Split-Luciferase System

  2012cited by this paper
• Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks

  2012cited by this paper
• Quantitative chemical proteomics approach to identify post-translational modification-mediated protein-protein interactions.

  2012cited by this paper
• Development and application of a DNA microarray-based yeast two-hybrid system

  2012cited by this paper
• A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data

  2012cited by this paper
• Analysis of stable and transient protein-protein interactions.

  2012cited by this paper
• Cluster-based assessment of protein-protein interaction confidence

  2012cited by this paper
• HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores

  2012cited by this paper
• Protein-protein interaction networks: unraveling the wiring of molecular machines within the cell.

  2012cited by this paper
• Benzodiazepines and benzotriazepines as protein interaction inhibitors targeting bromodomains of the BET family

  2012cited by this paper
• Interactome networks and human disease.

  2011cited by this paper
• Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme

  2011cited by this paper
• A comparison of the functional modules identified from time course and static PPI network data

  2011cited by this paper
• Transient protein-protein interactions.

  2011cited by this paper
• Global Geometric Affinity for Revealing High Fidelity Protein Interaction Network

  2011cited by this paper
• Predicting Functions of Proteins in Mouse Based on Weighted Protein-Protein Interaction Network and Protein Hybrid Properties

  2011cited by this paper
• Towards the prediction of protein interaction partners using physical docking

  2011cited by this paper
• Leveraging the power of next-generation sequencing to generate interactome datasets

  2011cited by this paper
• Building Protein-Protein Interaction Networks with Proteomics and Informatics Tools*

  2011cited by this paper
• Predicting protein–protein interactions from sequence using correlation coefficient and high-quality interaction dataset

  2010cited by this paper
• Discovering pathways by orienting edges in protein interaction networks

  2010cited by this paper
• Recent advances in clustering methods for protein interaction networks

  2010cited by this paper
• Link Prediction in Complex Networks: A Survey

  2010cited by this paper
• The structural basis of peptide-protein binding strategies.

  2010cited by this paper
• Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks

  2010cited by this paper
• Essential Proteins Discovery from Weighted Protein Interaction Networks

  2010cited by this paper
• The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

  2010cited by this paper
• New dimensions in the study of protein complexes using quantitative mass spectrometry

  2009cited by this paper
• Geometric De-noising of Protein-Protein Interaction Networks

  2009cited by this paper
• Protein dynamics and conformational disorder in molecular recognition

  2009cited by this paper
• Complex discovery from weighted PPI networks

  2009cited by this paper
• Influence of Protein Abundance on High-Throughput Protein-Protein Interaction Detection

  2009cited by this paper
• Prediction of Protein Binding Regions in Disordered Proteins

  2009cited by this paper
• Protein–protein interaction and quaternary structure

  2008cited by this paper
• Assessing and predicting protein interactions using both local and global network topological metrics.

  2008cited by this paper
• An experimentally derived confidence score for binary protein-protein interactions

  2008cited by this paper
• PIPs: human protein–protein interaction prediction database

  2008cited by this paper
• Quantitative assessment of the structural bias in protein–protein interaction assays

  2008cited by this paper
• Using support vector machine combined with auto covariance to predict protein–protein interactions from protein sequences

  2008cited by this paper
• Two-hybrid technologies in proteomics research.

  2008cited by this paper
• Fitting a geometric graph to a protein-protein interaction network

  2008cited by this paper
• Protein networks in disease.

  2008cited by this paper
• Hierarchical structure and the prediction of missing links in networks

  2008cited by this paper
• Coverage and error models of protein-protein interaction data by directed graph analysis

  2007cited by this paper
• PathFinder: mining signal transduction pathway segments from protein-protein interaction networks

  2007cited by this paper
• Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners

  2007cited by this paper
• WI‐PHI: A weighted yeast interactome enriched for direct physical interactions

  2007cited by this paper
• Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network

  2007cited by this paper

• Integrated experimental and computational approaches to analyze TNF superfamily ligand-receptor interactions.

  2026cites this paper
• A hybrid DNN model using novel integrated interface features for predicting protein-protein complexes binding affinity

  2025cites this paper
• Integrative Protein–Protein Interaction Network Analysis and Druggability Assessment of the Candidozyma auris Proteome for Novel Drug Target Identification

  2025cites this paper
• Decrypting the impact of ferroptosis and cuproptosis in development of pancreatic ductal adenocarcinoma

  2025cites this paper
• Towards a phylogenetically informed approach to solving protein–protein interactions

  2025cites this paper
• Benchmarking all-atom biomolecular structure prediction with FoldBench

  2025cites this paper
• Multimodal Learning of Protein–Protein Interactions for Accurate Binding Affinity Prediction

  2025cites this paper
• ESM2-Driven Protein-Protein Interaction Prediction with Global-Local Graph Topology Learning

  2025cites this paper
• Targeting YAP/TAZ-TEAD and their protein-protein interaction for precision cancer therapy.

  2025cites this paper
• MPBind: a multitask protein binding site predictor using protein language models and equivariant GNNs

  2025cites this paper
• MKLNID: Identifying Melanoma-related Pathogenic Genes Through Multiple Kernel Learning and Network Impulsive Dynamics.

  2025cites this paper
• Incorporating multi-scale module kernel for disease-gene identification in biological networks

  2025cites this paper
• An E. coli two-hybrid system to investigate human protein-protein interactions

  2025cites this paper
• Bacterial two-hybrid systems evolved: innovations for protein-protein interaction research

  2025influential citation
• A Survey of Biological Function Prediction Methods with Focus on Natural Language Processing (NLP) and Large Language Models (LLM).

  2025cites this paper
• Genome-wide and transcriptome analysis of PdWRKY transcription factors in date palm (Phoenix dactylifera) revealing insights into heat and drought stress tolerance

  2025cites this paper
• Phytopathogen Effector Biology in the Burgeoning AI Era.

  2025cites this paper
• Screening of Bioactive Compounds and Deep Learning-driven Quality Control of Angong Niuhuang Pills.

  2025cites this paper
• FoldBench: An All-atom Benchmark for Biomolecular Structure Prediction

  2025cites this paper
• PPI-Graphomer: enhanced protein-protein affinity prediction using pretrained and graph transformer models

  2025cites this paper
• Challenges in predicting protein-protein interactions of understudied viruses: Arenavirus-human interactions

  2025cites this paper
• MPBind: Multitask Protein Binding Site Prediction by Protein Language Models and Equivariant Graph Neural Networks

  2025cites this paper
• Genome-Wide Analysis of Vacuolar Iron Transporter (VIT) Gene Family in Phaseolus vulgaris L.: Functional Roles in Heavy Metal Stress

  2025cites this paper
• PRODE recovers essential and context-essential genes through neighborhood-informed scores

  2025cites this paper
• Genome-wide characterization of the PCO (Plant Cysteine ​​Oxidase) gene family in Phaseolus vulgaris L. and expression analysis under heavy metal stress

  2025cites this paper
• Predicting Which Mitophagy Proteins Are Dysregulated in Spinocerebellar Ataxia Type 3 (SCA3) Using the Auto-p2docking Pipeline

  2025cites this paper
• PPAP: A Protein-protein Affinity Predictor Incorporating Interfacial Contact-Aware Attention

  2025cites this paper
• Heterogeneous network impulsive dynamics for identifying disease-associated genes

  2024cites this paper
• EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks

  2024cites this paper
• HBFormer: a single-stream framework based on hybrid attention mechanism for identification of human-virus protein–protein interactions

  2024cites this paper
• Uncovering the domain language of protein functionality and cell phenotypes using DANSy

  2024cites this paper
• Taoren Honghua Decoction alleviates atherosclerosis by inducing autophagy and inhibiting the PI3K-AKT signaling pathway to regulate cholesterol efflux and inflammatory responses.

  2024cites this paper
• Identification of Host Factors Interacting with Movement Proteins of the 30K Family in Nicotiana tabacum

  2024cites this paper
• Pre-mRNA processing factor 4 kinases (PRP4Ks): Exploration of molecular features, interaction network and expression profiling in bread wheat

  2024cites this paper
• SPIDER: constructing cell-type-specific protein–protein interaction networks

  2024cites this paper
• Studying protein-protein interactions: Latest and most popular approaches.

  2024cites this paper
• Metabolic Proteins Expression Up-Regulated in Blood-Borne Extensively Drug-Resistant Salmonella Typhi Isolates from Pakistan

  2024cites this paper
• Malivhu: A Comprehensive Bioinformatics Resource for Filtering SARS and MERS Virus Proteins by Their Classification, Family and Species, and Prediction of Their Interactions Against Human Proteins

  2024cites this paper
• A New Framework for Pinpointing Crucial Proteins in Protein-Protein Interaction Networks

  2024cites this paper
• Structure based functional identification of an uncharacterized protein from Coxiella burnetii involved in adipogenesis

  2024cites this paper
• Introducing dysfunctional Protein-Protein Interactome (dfPPI) - A platform for systems-level protein-protein interaction (PPI) dysfunction investigation in disease.

  2024cites this paper
• Heterogeneous network approaches to protein pathway prediction

  2024cites this paper
• An Ensemble Classifiers for Improved Prediction of Native–Non-Native Protein–Protein Interaction

  2024cites this paper
• DDMut-PPI: predicting effects of mutations on protein–protein interactions using graph-based deep learning

  2024cites this paper
• Topology-driven negative sampling enhances generalizability in protein–protein interaction prediction

  2024cites this paper
• USP7 interacts with and destabilizes oncoprotein SET.

  2024cites this paper
• ProAffinity-GNN: A Novel Approach to Structure-based Protein-Protein Binding Affinity Prediction via a Curated Dataset and Graph Neural Networks

  2024cites this paper
• SAH is a major metabolic sensor mediating worsening metabolic crosstalk in metabolic syndrome

  2024cites this paper
• Leveraging machine learning models for peptide–protein interaction prediction

  2024cites this paper
• Uncovering domain motif interactions using high‐throughput protein–protein interaction detection methods

  2024cites this paper
• Identifying inflammation-related targets of natural lactones using network pharmacology, molecular modeling and in vitro approaches

  2024cites this paper
• Oral_voting_transfer: classification of oral microorganisms’ function proteins with voting transfer model

  2024cites this paper
• Proteome‐wide assessment of human interactome as a source of capturing domain–motif and domain‐domain interactions

  2024cites this paper
• Inferring Interaction Networks from Transcriptomic Data: Methods and Applications.

  2023cites this paper
• Deciphering sperm functions using biological networks

  2023cites this paper
• RF_phage virion: Classification of phage virion proteins with a random forest model

  2023cites this paper
• PIQLE: protein-protein interface quality estimation by deep graph learning of multimeric interaction geometries

  2023cites this paper
• Deep learning-assisted prediction of protein-protein interactions in Arabidopsis thaliana.

  2023cites this paper
• Protein Profiling in Human Papillomavirus-Associated Cervical Carcinogenesis: Cornulin as a Biomarker for Disease Progression

  2023cites this paper
• A systematic review of computational approaches to understand cancer biology for informed drug repurposing

  2023cites this paper
• Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models

  2023cites this paper
• Recent Updates on Interaction Studies and Drug Delivery of Antimalarials with Serum Albumin proteins.

  2023cites this paper
• Dynamic interplay of WRKY, GRAS, and ERF transcription factor families in tomato-endophytic fungal symbiosis: insights from transcriptome and genome-wide analysis

  2023cites this paper
• Large-scale data mining pipeline for identifying novel soybean genes involved in resistance against the soybean cyst nematode

  2023cites this paper
• PIQLE: protein–protein interface quality estimation by deep graph learning of multimeric interaction geometries

  2023cites this paper
• Seq-InSite: sequence supersedes structure for protein interaction site prediction

  2023cites this paper
• In Vitro Reconstitution and Analysis of SARS-CoV-2/Host Protein–Protein Interactions

  2023cites this paper
• Computational Approaches for Structure-Based Functional Annotation of an Uncharacterized Conserved Protein of Acinetobacter baumannii†

  2023cites this paper
• The Gene Network Correlation Analysis of Obesity to Type 1 Diabetes and Cardiovascular Disorders: An Interactome-Based Bioinformatics Approach

  2023cites this paper
• Identification of coastal pesticide pollutants as potent inhibitors of Bacillus pasteurii urease mediated calcium carbonate precipitation: a computational approach

  2023cites this paper
• TDP-43 protein interactome informs about perturbed canonical pathways and may help develop personalized medicine approaches for patients with TDP-43 pathology.

  2023cites this paper
• Prediction of transient and permanent protein interactions using AI methods

  2023cites this paper
• Leveraging Machine Learning Models for Peptide-Protein Interaction Prediction

  2023cites this paper
• NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation

  2023cites this paper
• Regulation of bacterial haem biosynthesis

  2022cites this paper
• Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context

  2022cites this paper
• In silico study reveals unconventional interactions between MDC1 of DDR and Beclin-1 of autophagy

  2022cites this paper
• Identification of Common Hub Genes in Human Dermal Fibroblasts Stimulated by Mechanical Stretch at Both the Early and Late Stages

  2022cites this paper
• Protein–Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation

  2022cites this paper
• Modeling the MreB-CbtA Interaction to Facilitate the Prediction and Design of Candidate Antibacterial Peptides

  2022cites this paper
• Interfacial Peptides as Affinity Modulating Agents of Protein-Protein Interactions

  2022cites this paper
• CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs

  2022cites this paper
• A Non-local Graph Neural Network for Identification of Essential Proteins

  2022cites this paper
• Structural Aspects of Protein–Protein Interactions

  2021cites this paper
• TIDB: a comprehensive database of trained immunity

  2021cites this paper
• PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data

  2021cites this paper
• Integrated network analysis identifying potential novel drug candidates and targets for Parkinson's disease

  2021cites this paper
• Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis

  2021cites this paper
• SETS: A Seed-Dense-Expanding Model-Based Topological Structure for the Prediction of Overlapping Protein Complexes

  2021cites this paper
• Posttranslational modifications in systems biology.

  2021cites this paper
• A scheme for inferring viral-host associations based on codon usage patterns identifies the most affected signaling pathways during COVID-19

  2021cites this paper
• HyMM: Hybrid method for disease-gene prediction by integrating multiscale module structures

  2021cites this paper
• NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction

  2021cites this paper
• Current status and future perspectives of computational studies on human-virus protein-protein interactions

  2021cites this paper
• Identification of Ku70 Domain-Specific Interactors Using BioID2

  2021cites this paper
• Interactions of the Receptor Binding Domain of SARS-CoV-2 Variants with hACE2: Insights from Molecular Docking Analysis and Molecular Dynamic Simulation

  2021cites this paper
• An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies

  2021cites this paper
• Bioinformatic analysis of differentially expressed genes and pathways in idiopathic pulmonary fibrosis

  2021cites this paper
• Investigating protein expression, modifications and interactions in the brain: Protocol for preparing rodent brain tissue for mass spectrometry-based quantitative- and phospho-proteomics analysis.

  2021cites this paper
• Open Circuit Potential as a Tool for the Assessment of Binding Kinetics and Reagentless Protein Quantitation.

  2021cites this paper